You haven’t provided the information requested, or any detail, so i can’t provide you with any detailed answer of exactly how you would do it. If you can provide more detail, people can probably provide you with better advice as to how to achieve what you want.

Further, it is even OK to show us a CSR (Certificate Signing Request) that you are hoping Let’s Encrypt will accept, these documents do not usually contain any secrets (there may be a “password” option, but you can leave it blank). They basically just spell out what certificate the application is asking for, and if there’s anything about that which Let’s Encrypt would find objectionable and you can’t change it in the application, then you’ll know without any further effort it can’t work.

A consideration, especially if you’re looking at Let’s Encrypt as a cost-saving choice or as an improvement over using self-signed certificates, is how convenient it will be for you to perform the renewal step ~5 times per year, as each certificate from Let’s Encrypt has validity of only 90 days. Most people using Let’s Encrypt are able to automate a renewal process, so that the short lifetime is no inconvenience at all, but if you need to do manual request and import steps in your proprietary application you may find this outweighs the benefit. Better to know now, than to regret the choice a few months from now.